The twists and turns of organic semiconductor chains: a single-molecule view of conjugated polymers in solution    A. Brenlla-Lopez,  Ifor D. W. Samuel and J. Carlos Penedo*. In preparation		2023
TWIN-FRET: overcoming the orthogonal chemistry labelling barrier using equilibrium-encoded FRET pairs S. Jana, M. Diez-Castellnou, S. Thomson,  M. Fossepre, M. Surin, Y. Olivier, E. Kay, J. Carlos Penedo* In preparation		2023
Energy transfer from end-terminal labelled polyfluorene molecules discriminates alpha and beta-phase content Alfonso Brenlla-Lopez,  Ifor D W Samuel J. Carlos Penedo To be submitted		2023
Zuo1 preferentially induces and stabilizes unstable G4 structures Ines Burkhart,  Michaela Limmer, J. Carlos Penedo, Harald Schwalbe and Katrin Paeschke To be submitted, Nat. Comm.		2023
Topographic fingerprinting of single proteins and proteoforms J. Carlos Penedo Nat. Nanotech, In revision		2023
Cotranscriptional folding of a 5' stem-loop in the Escherichia Coli tbpA riboswitch at single-nucleotide resolution Elsa D. M. Hien, Patrick St-Pierre, J. Carlos Penedo, Daniel A. Lafontaine Nucleic Acids Res, In revision		2023
Multiple intermediates in the detergent induced fusion of lipid vesicles L.G. Dresser, Casper Kunstmann, Donato Conteduca, STeven Johnson, J. Carlos Penedo, Mark C Leake, Steven D Quinn Communications materials, In revision		2023
Conformational rearrangements regulating DNA repair protein APE1 Nina Komaniecka, Marta Porras, Louis Cairn, Jon Ander Santas, Juan Carlos Penedo, Sonia Bañuelos * Int. J. Mol. Sci. 23(14) 8015		2022
Fatty acids may influence insulin actions through modulation of albumin-Zn2+ interactions Swati Ayra, Adam Gourley, J. Carlos Penedo, Claudia Blindauer, Alan Stewart*. Bioessays. 2021;2100172.		2021

Monitoring RNA dynamics within native transcriptional complexes  Adrien Chauvier, Patrick St-Pierre, Jean-François Nadon, Elsa DM Hien, Cibran Perez-Gonzalez, Sébastien H. Eschbach, Anne-Marie Lamontagne, J. Carlos Penedo* and Daniel A. Lafontaine*. Proc.Natl. Acad. Sci. USA. Accepted, September 2021		2021

A structural intermediate pre-organizes the add adenine riboswitch for ligand recognition P. St-Pierre, E. Shaw, S. Jacques,P. A. Dalgarno, C. Perez-Gonzalez, F. Picard-Jean, J. Carlos Penedo* and Daniel A. Lafontaine* Nucleic Acids Res. Published 8 May, doi:  10.1093/nar/gkab307		2021

The influence of various regions of the FOXP2 sequence on its structure and DNA binding function  Monare Thulo, Megan A. Rabie, Naadira Pahad, Heather L Donald, Ashleigh A Blane, Cardon M  Perumal, J. Carlos Penedo and Sylvia Fanucchi*   Biosci. Rep. doi.org/10.1042/BSR20202128 .		2020

Functional 3D architecture in an intrinsically disordered E3 ligase domain facilitates ubiquitin transfer Paul Murphy, Yingqi Xu, Sarah L. Rouse, Steve J. Matthews, J. Carlos Penedo, Ron T. Hay*. Nat. Communications, 11, Article number: 3807.		2020

Ubiquitin transfer by a RING E3 ligase occurs from a closed E2-Ub conformation Emma Branigan, J. Carlos Penedo*, Ron T. Hay*. Nat. Communications, 11, Article number: 2846		2020

Asymmetric base pair opening drives helicase unwinding dynamics Francesco Colizzi*, Cibran Perez-Gonzalez, Remi Fritzen, Yaakov Levy, Malcolm F. White, J. Carlos Penedo*, Giovanni Bussi*. Proc. Natl. Acad. Sci. USA (October 18, 2019 https://doi.org/10.1073/pnas.1901086116)		2019

Single-molecule spectroscopy of polyfluorene chains reveals beta-phase content and phase reversibility in organic solvents Alfonso Brenlla, Francisco Tenopala-Carmona, Alexander L. Kanibolotsky, Peter J. Skabara*, Ifor D. W. Samuel*, J. Carlos Penedo*. Matter (Cell Press), Published:October 09, 2019 DOI:https://doi.org/10.1016/j.matt.2019.07.020		2019

Unveiling the multi-step solubilization mechanism of sub-micron size vesicles by detergents Paul A. Dalgarno, Jose Juan Colas, Gordon J Hedley, Lucas Pineiro, Mercedes Novo, Cibran Perez-Gonzalez, Ifor D. W. Samuel, Mark C. Leake, Steven Johnson, Wajih Al-Soufi, J. Carlos Penedo* and Steven D. Quinn* Scientific Reports, 9:12897		2019

Unprecedented tunability of riboswitch structure and regulatory function by sub-millimolar variations in physiological Mg2+ Kaley McCluskey*, Julien Boudreault, Patrick St-Pierre, Cibran Perez-Gonzalez, Adrien Chauvier, Adrien Rizzi, Pascale B. Beauregard, Daniel A. Lafontaine* and J. Carlos Penedo*. Nucleic Acids Res. 47, 6478-6487		2019

Real-time observation of conformational switching in single conjugated polymers chains. F. Tenopala-Carmona, S. Fronk, G. Bazan*, I. D. W. Samuel* and J. Carlos Penedo* Science Advances, Vol. 4, no. 2, eaao5786		2018

DNA binding and unwinding of forked DNA by Hel308 requires dual functions of a winged helix domain. Sarah J Northall, Ryan Buckey, Nathan Jones, J. Carlos Penedo, Panos Soultanas and Edward Bolt. DNA repair, 57, 125-132		2017

Transcriptional dynamics Daniel A Lafontaine*, J. Carlos Penedo*. Editorial preface special topic in 'Transcriptional dynamics' Methods, Vol 120, 1-2		2017

An integrated perspective on RNA aptamer ligand recognition models: clearing muddy waters Kaley McCluskey*, J. Carlos Penedo*. Phys. Chem. Chem. Phys. In press doi: 10.1039/C6CP08798A		2017
High affinity RNA binding by a hyperthermophilic single-stranded DNA binding protein Michael Morten, Roland Gamsjaeger, Ruvini Kariawasam, Liza Cubeddu, Jose Peregrina, Elena Evgureieva-Hackenberg, J. Carlos Penedo and Malcolm F. White. Extremophiles. doi:10.1007/s00792-016-0910-2		2017

Fluorescence-based strategies to investigate the structure and dynamics of RNA aptamer-ligand complexes Cibran Perez-Gonzalez, Daniel A. Lafontaine*, J. Carlos Penedo* Frontiers in Chemistry, special topic in Natural and artificially-engineered nucleic acid aptamers: design, characterization and technological applications: Eds. Daniel A. Lafontaine and J. Carlos Penedo, Front. Chem. doi: 10.3389/fchem.2016.00033		2016
Morphology-specific inhibition of b-amyloid aggregates by 17b-hydroxysteroid dehydrogenase type 10 Laura Aitken, Steven D. Quinn, Daniel C. Perez-Gonzalez, Ifor D. W. Samuel, J. Carlos Penedo* and Frank Gunn-Moore* ChemBioChem. 17, 1029-1037.		2016

Biophysical approaches to bacterial gene regulation by riboswitches Cibran Perez-Gonzalez, Daniel A. Lafontaine* and J. Carlos Penedo* Advances in Experimental Medicine and Biology, 915, 157-191		2016
Mechanism of DNA loading by the DNA repair helicase XPD Diana Constantinescu Aruxandei, Biljana Petrovic-Stojanovska, J. Carlos Penedo, Malcolm F. White and James Naismith Nucl. Acids Res. (2016) doi: 10.1093/nar/gkw102		2016

Binding dynamics of a monomeric SSB protein to DNA: a single-molecule multi-process approach Michael J. Morten, Jose R. Peregrina, Maria Figueira-Gonzalez, Katrin Ackermann, Bela E Bode, Malcolm F. White* and J. Carlos Penedo* Nucleic Acids Res. 43(22), 10907-10924		2015

Functional Studies of DNA-Protein Interactions Using FRET Techniques S Blouin, TD Craggs, DA Lafontaine, JC Penedo DNA-Protein Interactions, Methods in Molecular Biology, 115-141		2015
Single-molecule approaches for the characterization of riboswitch folding mechanisms Julien Boudreault, D. Cibran Perez-Gonzalez, J. Carlos Penedo and Daniel A. Lafontaine. DNA-Protein interactions: Methods and Protocols. Methods Mol. Biol. Vol 1334, 115-141		2015
Single-molecule strategies for DNA and RNA diagnostics D. Cibran Perez-Gonzalez, J. Carlos Penedo, RNA Technologies: RNA and DNA diagnostics. Springer-Verlag. Eds (D. A. Erdmann, S. Jurga and J. Barciszweski) pp 297-332		2015
Towards ratiometric sensing of amyloid fibrils in vitro Sonia Freire, Flor Rodriguez-Prieto, M. Carmen Rios Rodriguez, J. Carlos Penedo, Wajih Al-Soufi and Mercedes Novo*, Chemistry- A European Journal, 21, 3425 – 3434		2015
Using smFRET and denaturants to reveal folding landscapes E. Shaw, K. McCluskey, P. St-Pierre, Daniel A. Lafontaine* and J. Carlos Penedo* Methods in Enzymology. Vol. 549, 313-341		2014
Phosphorylation of Hsp20 enhances its association with beta-amyloid to increase protection against neuronal cell death Ryan T. Cameron, Steven D. Quinn, Lynn S. Z. Cairns, Ruth MacLeod, Brian O. Smith,Ifor D. W. Samuel, J. Carlos Penedo and George S. Baillie.Molecular and Cellular Neurosciences. In press .DOI: 1016/j.mcn.2014.05.002		2014
Fluorescence tools to investigate riboswitch structural dynamics P. St-Pierre, K. McCluskey, E. Shaw, J. Carlos Penedo* and Daniel A Lafontaine*.BBA-Gene regulatory Mechanisms. In press. DOI: 10.1016/j.bbagrm.2014.05.015		2014
Single-molecule characterization of Fen1 and Fen1/PCNA complexes acting on flap substrates Timothy D. Craggs, Richard D. Hutton, Alfonso Brenlla, Malcolm F. White and J. Carlos Penedo, Nucleic Acids Res. doi: 10.1093/nar/gkt1116		2014
Single-Molecule Fluorescence of Nucleic Acids K McCluskey, E Shaw, DA Lafontaine, JC Penedo Fluorescence Spectroscopy and Microscopy, Methods in Molecular Biology,1076 759-791		2013
Real-time probing of amyloid aggreation and inhibition using fluorescence self-quenching between neighbouring dyes SD Quinn, PA Dalgarno, RT Cameron, GJ Hedley, C Hacker, JM Lucocq, GS Baillie, IDW Samuel, JC Penedo.Mol. BioSyst., 2014, 10 (1), 34 - 44		2013
Solution-Based Single Molecule Imaging of Surface-Immobilized Conjugated Polymers PA Dalgarno, CA Traina, JC Penedo, GC Bazan, IDW Samuel Journal of the American Chemical Society		2013
Single-molecule chemical denaturation of riboswitches PA Dalgarno, J Bordello, R Morris, P St-Pierre, A Dubé, IDW Samuel, DA, Daniel A. Lafontaine and J. Carlos Penedo Nucleic acids research		2013
Folding of the SAM-I riboswitch: A tale with a twist SH Eschbach, P St-Pierre, JC Penedo, DA Lafontaine RNA Biology 9 (5), 535-541		2012
Constitutive regulatory activity of an evolutionarily excluded riboswitch variant R Tremblay, JF Lemay, S Blouin, J Mulhbacher, É Bonneau, P Legault, P Dupont ... Journal of Biological Chemistry 286 (31), 27406-27415		2011
Molecular insights into the ligand-controlled organization of the SAM-I riboswitch B Heppell, S Blouin, AM Dussault, J Mulhbacher, E Ennifar, JC Penedo, DA ... Nature Chemical Biology 7 (6), 384-392		2011
PCNA and XPF cooperate to distort DNA substrates RD Hutton, TD Craggs, MF White, JC Penedo Nucleic acids research 38 (5), 1664-1675		2010
Riboswitches: ancient and promising genetic regulators S Blouin, J Mulhbacher, JC Penedo, DA Lafontaine Chembiochem 10 (3), 400-416		2009
Natural Functional Nucleic Acids: Ribozymes and Riboswitches R Tremblay, J Mulhbacher, S Blouin, JC Penedo, DA Lafontaine Functional Nucleic Acids for Analytical Applications, 11-46		2009
Functional Studies of DNA-Protein Interactions Using FRET Techniques S Blouin, TD Craggs, DA Lafontaine, JC Penedo DNA-Protein Interactions, Methods in Molecular Biology, 475-502		2009
Molecular basis of RNA-mediated gene regulation on the adenine riboswitch by single-molecule approaches JF Lemay, JC Penedo, J Mulhbacher, DA Lafontaine Riboswitches, Methods in Molecular Biology, 65-76		2009
Application of fluorescent measurements for characterization of riboswitch–ligand interactions B Heppell, J Mulhbacher, JC Penedo, DA Lafontaine Riboswitches, Methods in Molecular Biology,25-37		2009
PCNA stimulates catalysis by structure-specific nucleases using two distinct mechanisms: substrate targeting and catalytic step RD Hutton, JA Roberts, JC Penedo, MF White Nucleic acids research 36 (21), 6720-6727		2008
Solvent dependent photophysics of fac-[Re (CO) 3 (11, 12-X2dppz)(py)]+(X= H, F or Me) J Dyer, CM Creely, JC Penedo, DC Grills, S Hudson, P Matousek, AW Parker, M Photochemical & Photobiological Sciences 6 (7), 741-748		2007
Folding of the adenine riboswitch JF Lemay, JC Penedo, R Tremblay, DMJ Lilley, DA Lafontaine Chemistry & Biology 13 (8), 857-868		2006
Two competitive routes in the lactim-lactam phototautomerization of a hydroxypyridine derivative cation in water: dissociative mechanism versus water-assisted proton transfer JC Penedo, MC Ríos Rodríguez, I García Lema, JL Pérez Lustres, M Mosquera, F ... The Journal of Physical Chemistry A 109 (45), 10189-10198		2005
Photophysical study of a family of [Ru (phen) 2 (Mendpq)] 2+ complexes in different solvents and DNA: a specific water effect promoted by methyl substitution K O'Donoghue, JC Penedo, JM Kelly, PE Kruger Dalton Transactions, 1123-1128		2005
Solvent-dependent ground-and excited-state tautomerism in 2-(6'-hydroxy-2'-pyridyl) benzimidazole JC Penedo, JLP Lustres, IG Lema, MCR Rodríguez, M Mosquera, F Rodríguez-Prieto The Journal of Physical Chemistry A 108 (29), 6117-6126		2004
Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements JC PENEDO, TJ WILSON, SD JAYASENA, A KHVOROVA, DMJ LILLEY RNA 10 (5), 880-888		2004
Ultrafast transient absorption studies of ruthenium and rhenium dipyridophenazine complexes bound to DNA and polynucleotides CM Creely, JM Kelly, MM Feeney, S Hudson, JC Penedo, WJ Blau, B Elias, A ... OPTO Ireland, Proceedings SPIE, 92-102		2003
Role of hydrogen-bonded adducts in excited-state proton-transfer processes JC Penedo, M Mosquera, F Rodríguez-Prieto The Journal of Physical Chemistry A 104 (32), 7429-7441		2000
On the Mechanism of Alcohol-Catalyzed Excited-State Intramolecular Proton Transfer in Cationic Benzimidazoles MCR Rodríguez, JC Penedo, RJ Willemse, M Mosquera, F Rodríguez-Prieto The Journal of Physical Chemistry A 103 (36), 7236-7243		1999
Solvent control of molecular structure and excited-state proton-transfer processes of 1-methyl-2-(2′-hydroxyphenyl)-benzimidazole F Rodríguez-Prieto, JC Penedo, M Mosquera Journal of the Chemical Society, Faraday Transactions 94 (18), 2775-2782		1998
Photoinduced Inter-and Intramolecular Proton Transfer in Aqueous and Ethanolic Solutions of 2-(2'-Hydroxyphenyl) benzimidazole: Evidence for Tautomeric and Conformational Equilibria in the Ground State M Mosquera, JC Penedo, MC Ríos Rodríguez, F Rodríguez-Prieto The Journal of Physical Chemistry 100 (13), 5398-5407		1996